   16  ./vmware-install.pl
   17  auto-install perl
   18  sudo install perl
   19  fastqc
   20  sudo apt install perl
   21  tar zxvf VMwareTools-10.1.15-6627299.tar.gz
   22  cp -r * ~/here
   23  cd
   24  cd ~/here
   25  tar zxvf VMwareTools-10.3.10-12406962.tar.gz 
   26  cd vmware-tools-distrib/
   27  ll
   28  head vmware-install.pl 
   29  head -100 vmware-install.pl 
   30  ./vmware-install.pl 
   31  sudo ./vmware-install.pl
   32  cd
   33  cd download/
   34  wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
   35  bash Miniconda3-latest-Linux-x86_64.sh 
   36  conda --version
   37  java
   38  sudo apt install default-jre
   39  sudo apt install openjdk-8-jre-headless
   40  sudo apt install openjdk-11-jre-headless
   41  conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
   42  conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/
   43  conda config --set show_channel_urls yes
   44  conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud//pytorch/
   45  conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/
   46  conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/msys2/
   47  conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/
   48  conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/menpo/
   49  conda create -n py36 python=3.6
   50  conda activate py36
   51  conda env list
   52  conda create -n py36 python=3.6
   53  conda update -n base -c defaults conda
   54  conda create -n py36 python=3.6
   55  conda activate py36
   56  conda install bwa
   57  conda install hisat2
   58  conda cearch bowtie2
   59  conda search bowtie2
   60  conda install star
   61  conda search bowtie2
   62  conda install bowtie2=2.3.0
   63  bowtie2 -h
   64  STAR -h
   65  bwa -h
   66  hisat2 -h
   67  conda list
   68  conda search samtools
   69  conda create -n bio
   70  conda activate bio
   71  conda install samtools
   72  conda install sra-tools
   73  conda activate py36
   74  conda search featurecounts
   75  featurecounts
   76  conda search subreads
   77  java
   78  sudo apt install openjdk-8-jre-headless
   79  sudo apt install default-jre
   80  sudo apt install openjdk-11-jre-headless
   81  java
   82  sudo apt install default-jre
   83  conda activate py36
   84  conda search subreads
   85  conda install subreads
   86  conda search htseq
   87  conda install htseq
   88  conda install subread
   89  featurecounts -h
   90  subread -h
   91  conda list
   92  featureCounts -h
   93  conda activate bio
   94  prefetch -h
   95  conda list
   96  conda activate py36
   97  conda install fastqc
   98  conda install multiqc
   99  df -lh
  100  cd /mnt
  101  ll
  102  cd hgfs/Ubunsave/
  103  ll
  104  conda activate py36
  105  cd index/
  106  ll
  107  bwa index -a bwtsw  hg19.fa
  108  cd bowtie2/
  109  bowtie2-build ../hg19.fa hg19.fa
  110  ll
  111  bowtie2  -x hg19.fa -U /home/yuan/data/dna/ENCFF283GNM.fastq -S eg1.sam
  112  bowtie2  -x hg19 -U /home/yuan/data/dna/ENCFF283GNM.fastq -S eg1.sam
  113  cd ../bwa/
  114  ll
  115  bwa mem hg19.fa /home/yuan/data/dna/ENCFF283GNM.fastq > aln-se.sam
  116  cd ../hisat2/
  117  hisat2-build ../hg19.fa hg19
  118  ll
  119  hisat2 -x hg19  -U /home/yuan/data/dna/ENCFF283GNM.fastq -S align.sam
  120  cd ../
  121  cd star/
  122  STAR --runMode genomeGenerate --genomeDir /home/yuan/index/star/ --genomeFastaFiles ../hg19.fa
  123  STAR --runMode genomeGenerate --genomeDir /home/yuan/index/star/ --genomeFastaFiles ../hg19.fa --genomeChrBinNbits 10
  124  conda install star=Estimated genome size=3338210368   3137210368   201000000
  125  conda search star
  126  log2(775)
  127  conda create -n star
  128  conda activate py36
  129  history
  130  hisat2 -x /home/yuan/index/hisat2/hg19  -U /home/yuan/data/dna/ENCFF283GNM.fastq -S /home/yuan/data/dna/ENCFF283GNM-hisat2/ENCFF283GNM.sam
  131  cd index/
  132  ll
  133  STAR --runMode genomeGenerate --genomeDir /home/yuan/index/star/ --genomeFastaFiles ../hg19.fa --genomeChrBinNbits 15
  134  STAR --runMode genomeGenerate --genomeDir /home/yuan/index/star/ --genomeFastaFiles hg19.fa --genomeChrBinNbits 15
  135  conda activate star
  136  sudo apt-get update
  137  sudo apt-get install g++
  138  sudo apt-get install make
  139  STAR --runMode genomeGenerate --runThreadN 1 --genomeDir /home/yuan/index/star/ --genomeFastaFiles hg19.fa --genomeChrBinNbits 15 
  140  conda install star=2.5.0c
  141  STAR --runMode genomeGenerate --runThreadN 1 --genomeDir /home/yuan/index/star/ --genomeFastaFiles hg19.fa --genomeChrBinNbits 15 
  142  ll
  143  grep "^>" hg19.fa | wc -l
  144  STAR --runMode genomeGenerate --runThreadN 1 --genomeDir /home/yuan/index/star/ --genomeFastaFiles hg19.fa --genomeChrBinNbits 6 
  145  STAR --runMode genomeGenerate --runThreadN 1 --genomeDir /home/yuan/index/star/ --genomeFastaFiles hg19.fa --genomeChrBinNbits 5
  146  STAR --runMode genomeGenerate --runThreadN 1 --genomeDir /home/yuan/index/star/ --genomeFastaFiles hg19.fa --genomeChrBinNbits 4
  147  STAR --runMode genomeGenerate --runThreadN 1 --genomeDir /home/yuan/index/star/ --genomeFastaFiles hg19.fa --genomeChrBinNbits 2
  148  STAR --runMode genomeGenerate --runThreadN 1 --genomeDir /home/yuan/index/star/ --genomeFastaFiles hg19.fa --genomeChrBinNbits 8
  149  df -lh
  150  ll
  151  cd
  152  grep "^>" /mnt/hgfs/Ubunsave/GRCh38.p13.genome.fa/GRCh38.p13.genome.fa | wc -l
  153  STAR --runMode genomeGenerate --runThreadN 1 --genomeDir /home/yuan/index/star/ --genomeFastaFiles /mnt/hgfs/Ubunsave/GRCh38.p13.genome.fa/GRCh38.p13.genome.fa
  154  conda activate bio
  155  conda remove -n env_name --all
  156  conda remove -n star --all
  157  conda activate py36
  158  conda list
  159  conda remove star
  160  conda install multiqc
  161  conda activate bio
  162  conda list
  163  conda install sra-toolkit
  164  conda search sra-toolkit
  165  conda activate py36
  166  bowtie2 -p 6 -3 5 --local -x mm10 -1 example_1.fastq -2 example_2.fastq -S SRR3208744.bam
  167  bowtie2  -3 5 --local -x /home/yuan/index/bowtie2/hg19 -U /home/yuan/data/dna/ENCFF283GNM.fastq -S /home/yuan/data/dna/ENCFF283GNM-bowtie2/ENCFF283GNM.sam
  168  bwa mem /home/yuan/index/bwa/hg19.fa /home/yuan/data/dna/ENCFF283GNM.fastq > /home/yuan/data/dna/bwa/ENCFF283GNM.sam
  169  conda activate py36
  170  conda list
  171  featureCounts -g gene_name -a /mnt/hgfs/Ubunsave/gencode.v33.annotation.gtf -o /home/yuan/data/dna/bowtie2/counts.txt /home/yuan/data/dna/bowtie2/ENCFF283GNM.sam
  172  featureCounts -g gene_name -a /mnt/hgfs/Ubunsave/gencode.v33.annotation.gtf -o /home/yuan/data/dna/bwa/counts.txt /home/yuan/data/dna/bwa/ENCFF283GNM.sam
  173  featureCounts -g gene_name -a /mnt/hgfs/Ubunsave/gencode.v33.annotation.gtf -o /home/yuan/data/dna/hisat2/hisat2.txt /home/yuan/data/dna/hisat2/ENCFF283GNM.sam
  174  conda activate bio
  175  samtools view -bS /home/yuan/data/dna/hisat2/ENCFF283GNM.sam > /home/yuan/data/dna/hisat2/ENCFF283GNM.bam
  176  samtools view -bS /home/yuan/data/dna/bwa/ENCFF283GNM.sam > /home/yuan/data/dna/bwa/ENCFF283GNM.bam
  177  samtools view -bS /home/yuan/data/dna/bowtie2/ENCFF283GNM.sam > /home/yuan/data/dna/bowtie2/ENCFF283GNM.bam
  178  conda activate bio
  179  conda search RIsearch
  180  RIsearch
  181  conda search RIsearch
  182  conda install RIsearch
  183  cd
  184  cdb
  185  cd bio/
  186  ll
  187  tar -xzvf RIsearch-1.1.tar.gz
  188  cd RIsearch-1.1/
  189  make
  190  /home/yuan/bio/RIsearch-1.1/RIsearch -q LINC01234_NR_110025.1.fasta -t gencode.v31.transcripts.fa -e -40 > TargetGene_LINC01234_trans_f40.txt
  191  cd /mnt/hgfs/Ubunsave/lncRNA_cis_trans5/trans
  192  ll
  193  /home/yuan/bio/RIsearch-1.1/RIsearch -q LINC01234_NR_110025.1.fasta -t gencode.v31.transcripts.fa -e -40 > TargetGene_LINC01234_trans_f40.txt
  194  cd
  195  cd shell/
  196  vim first.sh
  197  sudo apt install vim
  198  vim first.sh
  199  ll
  200  sh first.sh 
  201  cd /bin
  202  ll
  203  which vim
  204  cd
  205  cd /usr/bin/
  206  ls -lh
  207  conda activate py36
  208  python -u "/home/yuan/python/threetest.py"
  209  cd /mnt/hgfs/Ubunsave/lncRNA_cis_trans5/trans
  210  /home/yuan/bio/RIsearch-1.1/RIsearch -q LINC01234_NR_110025.1.fasta -t gencode.v31.transcripts.fa -e -40 > /home/yuan/data/lncrna/TargetGene_LINC01234_trans_f40.txt
  211  cd /home/yuan/data/lncrna/
  212  ll
  213  grep -iC 5 'free' TargetGene_LINC01234_trans_f40.txt > TargetGene_LINC01234_trans_f402.txt
  214  ll
  215  grep -i '^query' TargetGene_LINC01234_trans_f402.txt > TargetGene_LINC01234_trans_f403.txt
  216  ll
  217  cd /mnt/hgfs/Ubunsave/lncRNA_cis_trans5/trans/
  218  /home/yuan/bio/RIsearch-1.1/RIsearch -q LINC01234_NR_110025.1.fasta -t gencode.v31.transcripts.fa -e -20 > /home/yuan/data/lncrna/TargetGene_LINC01234_trans_f20.txt
  219  cd
  220  cd biosoft/
  221  ll
  222  tar -xzvf RIsearch-1.1.tar.gz
  223  cd RIsearch-1.1/
  224  make
  225  cd biosoft/
  226  cd
  227  cd biosoft/
  228  ll
  229  tar -xzvf RIsearch-1.1.tar.gz
  230  cd RIsearch-1.1/
  231  make
  232  cd
  233  cd /mnt/hgfs/Ubunsave/lncRNA_cis_trans5/trans
  234  /home/yuan/biosoft/RIsearch-1.1/RIsearch -q LINC01234_NR_110025.1.fasta -t gencode.v31.transcripts.fa -e -20 > /home/yuan/data/lncrna/TargetGene_LINC01234_trans_f20.txt
  235  cd
  236  cd data/lncrna/
  237  ll
  238  grep -i '^query' TargetGene_LINC01234_trans_f202.txt > TargetGene_LINC01234_trans_f203.txt
  239  df -lh
  240  conda activate py36
  241  cd python/
  242  ll
  243  python -u '/home/yuan/python/foru.py'
  244  python -u '/home/yuan/python/twotest.py'
  245  df -lh
  246  conda activate py36
  247  pip --version
  248  pip list
  249  prefetch --option-file SRR_Acc_List.txt
  250  cd data/
  251  conda activate bio
  252  prefetch --option-file SRR_Acc_List.txt
  253  df -lh
  254  history
  255  conda ebv list
  256  conda env list
  257  conda activate py336
  258  conda activate py36
  259  conda list
  260  conda activate bio
  261  conda list
  262  df -lh
  263  conda env list
  264  conda activate bio
  265  conda list
  266  conda activate py36
  267  conda list
  268  conda create -n py27 python=2.7
  269  conda insatll gdc-client
  270  conda install gdc-client
  271  conda activate py27
  272  conda install gdc-client
  273  cd tcga/
  274  ll
  275  gdc-client download -m gdc_manifest_20200501_100709.txt 
  276  df -lh
  277  history
  278  cd perl/
  279  vim first.pl
  280  perl first.pl 
  281  vim first.pl 
  282  perl first.pl 
  283  pip -v
  284  pip list
  285  conda env list
  286  conda eva list
  287  conda env list
  288  conda activate bio
  289  conda list
  290  conda activate py36
  291  conda list
  292  conda activate py27
  293  conda list
  294  history
  295  cd perl/
  296  perl first.pl 
  297  cd ../shell/
  298  bash first.sh 
  299  cd ../python/
  300  ls
  301  python p.py 
  302  python twotest.py 
  303  python threetest.py 
  304  h5st6ry
  305  history
  306  conda env list
  307  conda activate py36
  308  conda list
  309  bowtie2 -h
  310  ps
  311  cd data/GEO/rawdata/
  312  ls
  313  wget https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE54388&format=file
  314  wget -c https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE54388&format=file
  315  ps
  316  conda env list
  317  conda activate bio
  318  conda list
  319  conda activate py36 
  320  conda list
  321  history
  322  cd index/bowtie2/
  323  ls
  324  bowtie2  -x hg19 -U /home/yuan/data/dna/ENCFF283GNM.fastq -S eg1.sam
  325  isat2 -x /home/yuan/index/hisat2/hg19  -U /home/yuan/data/dna/ENCFF283GNM.fastq -S /home/yuan/data/dna/ENCFF283GNM-hisat2/ENCFF283GNM.sam
  326  hisat2 -x /home/yuan/index/hisat2/hg19  -U /home/yuan/data/dna/ENCFF283GNM.fastq -S /home/yuan/data/dna/ENCFF283GNM-hisat2/ENCFF283GNM.sam
  327  hisat2 -x /home/yuan/index/hisat2/hg19  -U /home/yuan/data/dna/ENCFF283GNM.fastq -S /home/yuan/data/dna/hisat2/ENCFF283GNM.sam
  328  bwa mem /home/yuan/index/bwa/hg19.fa /home/yuan/data/dna/ENCFF283GNM.fastq > /home/yuan/data/dna/bwa/ENCFF283GNM.sam
  329  history
  330  bowtie2  -3 5 --local -x /home/yuan/index/bowtie2/hg19 -U /home/yuan/data/dna/ENCFF283GNM.fastq -S /home/yuan/data/dna/ENCFF283GNM-bowtie2/ENCFF283GNM.sam
  331  bowtie2  -3 5 --local -x /home/yuan/index/bowtie2/hg19 -U /home/yuan/data/dna/ENCFF283GNM.fastq -S /home/yuan/data/dna/bowtie2/ENCFF283GNM.sam
  332  history
  333  conda activate py36
  334  bowtie2  -3 5 --local -x /home/yuan/index/bowtie2/hg19 -U /home/yuan/data/dna/ENCFF283GNM.fastq -S /home/yuan/data/dna/bowtie2/ENCFF283GNM.sam
  335  ls
  336  cd perl/
  337  ls
  338  perl first.pl
  339  cd ../python/
  340  ls
  341  cat p.py 
  342  less twotest.py 
  343  less firsttest.py 
  344  less foru.py 
  345  ls
  346  python rose.py 
  347  cd ../
  348  ls
  349  cd shell/
  350  ls
  351  less first.sh 
  352  shell *.sh
  353  sh *.sh
  354  cd perl/
  355  ls
  356  conda list
  357  pip -v
  358  pip install idna
  359  idna
  360  idna -v
  361  idna -help
  362  x-special/nautilus-clipboard
  363  copy
  364  file:///tmp/VMwareDnD/9KprGG/rose.py
  365  perl /home/yuan/perl/metadata.pl /home/yuan/data/GDC/clinical.cart.2019-09-28.json out.txt
  366  perl /home/yuan/perl/metadata.pl /home/yuan/data/GDC/clinical.cart.2020-06-09.json /home/yuan/data/GDC/ovarian.txt
  367  perl /home/yuan/perl/metadata.pl /home/yuan/data/GDC/metadata.cart.2020-06-09.json /home/yuan/data/GDC/ovarian2.txt
  368  which bash
  369  ls
  370  cd shell/
  371  ls
  372  vim one.sh
  373  cat one.sh 
  374  sh one.sh 
  375  vim one.sh 
  376  sh one.sh 
  377  ls
  378  one.sh
  379  ./one.sh
  380  sh one.sh 
  381  vim test2.sh
  382  sh test2.sh 
  383  vim test2.sh
  384  sh test2.sh 
  385  vim test2.sh
  386  sh test2.sh 
  387  vim test2.sh
  388  sh test2.sh 
  389  vim test2.sh
  390  sh test2.sh 
  391  vim test2.sh
  392  sh test2.sh 
  393  vim test3.sh
  394  sh test3.sh 
  395  conda env list
  396  conda activate py36
  397  conda list
  398  conda search trinity
  399  which perl
  400  perl -v
  401  perldoc
  402  apt install perl-doc
  403  perldoc -u -f atan2
  404  install perl-doc
  405  install --help
  406  apt-get install perl-doc
  407  install perl
  408  apt install perl
  409  apt-get perl-doc
  410  sudo apt-get install perl-doc
  411  perldoc -u -f atan2
  412  cd perl/
  413  vim one.pl
  414  one.pl
  415  perl one.pl 
  416  vim one.pl 
  417  perl one.pl 
  418  conda env list
  419  cd perl
  420  ls
  421  vim two.pl
  422  perl two.pl 
  423  vim two.pl
  424  perl two.pl 
  425  cd perl
  426  ls
  427  cat first.pl 
  428  rm first.pl 
  429  ls
  430  cay one.pl 
  431  cat one.pl 
  432  rm one.pl 
  433  cat two.pl 
  434  perl two.pl 
  435  ls
  436  perl Multiply.pl 
  437  perl Multiply.pl 12 12
  438  vim clinical.pl 
  439  ./train1.pl 
  440  ./perimeter.pl 
  441  perl Multiply.pl -12 -12
  442  ./Multiply.pl 12 12
  443  vim pcre.pl
  444  ./perimeter.pl 
  445  vim pcre.pl
  446  ./perimeter.pl 
  447  vim pcre.pl
  448  ./perimeter.pl 
  449  vim pcre.pl
  450  perl pcre.pl 
  451  vim pcre.pl
  452  perl pcre.pl  "yu"
  453  ./perimeter.pl "12" "12"
  454  perl pcre.pl  "yu{2}n"
  455  perl pcre.pl  "yu.n"
  456  perl pcre.pl  "yu.*n"
  457  perl pcre.pl  "(.)\1"
  458  vim clinical.pl 
  459  ls
  460  perl pcre.pl  "(.)\1"
  461  perl pcre.pl  "(.)\g{1}"
  462  perl pcre.pl  "(.)\g{1}11"
  463  perl pcre.pl  "jh|jr"
  464  vim bind.pl 
  465  perl bind.pl "123"
  466  vim bind.pl 
  467  perl bind.pl 
  468  vim bind.pl 
  469  perl bind.pl 
  470  vim bind.pl 
  471  perl bind.pl 
  472  perl bind.pl "ye"
  473  perldoc Digest::SHA
  474  perldoc Llamas
  475  cpan -D Digest::SHA
  476  perldoc -f -X
  477  history
  478  ls
  479  history > log.txt
  480  cd index/est/bwa/
  481  ls
  482  bwa index ../est.fa 
  483  conda env list
  484  conda activate bio
  485  conda list
  486  conda activate py36
  487  conda list
  488  bwa index ../est.fa 
  489  bowtie2-build ../est.fa est
  490  cd
  491  cd index/Arabidopsis/bwa/
  492  bwa indwx ../Arabidopsis.fa 
  493  bwa index ../Arabidopsis.fa 
  494  cd ../bowtie2/
  495  bowtie2-build ../Arabidopsis.fa Arabidopsis
  496  bowtie2-build ../Arabidopsis.fa.sa Arabidopsis
  497  bowtie2-build ../Arabidopsis.fa Arabidopsis
  498  cd ../hista2/
  499  hisat2-build ../Arabidopsis.fa Arabidopsis
  500  cd
  501  cd index/est/hista2/
  502  hisat2-build ../est.fa est
  503  cd
  504  cd data/human/dna/hisat2/
  505  ls
  506  cd ../bwa/
  507  ls
  508  head counts.txt
  509  cd /mnt/hgfs/Ubunsave/
  510  head /mnt/hgfs/Ubunsave/gtex_RSEM_gene_fpkm
  511  head -2 /mnt/hgfs/Ubunsave/gtex_RSEM_gene_fpkm
  512  cd perl/
  513  ls
  514  vim clinical.pl 
  515  vim GETx.pl
  516  cd /mnt/hgfs/Ubunsave/
  517  file /mnt/hgfs/Ubunsave/gtex_RSEM_gene_fpkm
  518  ls
  519  cd getGTExNormal/
  520  ls
  521  head -1 gtex_RSEM_gene_fpkm.txt 
  522  clear
  523  ls
  524  perl GTExNormal.pl 
  525  vim *.pl
  526  cat GTExSymbol.txt > GTExSymbol2.txt 
  527  ls
  528  perl GTEx.getGTExNormal.pl
  529  vim *.pl
  530  perl GTEx.getGTExNormal.pl
  531  vim *.pl
  532  perl GTEx.getGTExNormal.pl
  533  vim *.pl
  534  head -1 GTExSymbol.txt > head.txt
  535  vim *.pl
  536  perl GTEx.getGTExNormal.pl
  537  cd /mnt/hgfs/Ubunsave/getGTExNormal
  538  ls
  539  cat GTExNormalExp.txt | tr "[[:space:]]" "\t" > GTExNormalExp.csv
  540  ls
  541  ls -lh
  542  cat GTExSymbol.txt | tr "[[:space:]]" "\t" > GTExSymbol.csv
  543  sed '1,4p' GTExSymbol.csv | awk {print $1,$2}
  544  sed '1,4p' GTExSymbol.csv | awk {print '$1','$2'}
  545  sed '1,4p' GTExSymbol.csv | awk '{print $1,$2}'
  546  sed -n '1,4p' GTExSymbol.csv | awk '{print $1,$2}'
  547  sed -n '2,1p' GTExSymbol.csv | awk '{print $1,$2}'
  548  head -1 GTExSymbol.csv
  549  clear
  550  ls
  551  history
  552  clear
  553  ls
  554  file GTExSymbol.csv
  555  sed -i "s/,/\t/g" GTExSymbol.csv
  556  cat -A GTExSymbol.csv
  557  cat -A GTExSymbol.txt 
  558  sed -i "s/\t/ /g" GTExSymbol.csv
  559  cat -A GTExSymbol.csv
  560  ls
  561  sed -i "s/\t/ /g" TCGA-OV.htseq_fpkm.tsv 
  562  cat -A TCGA-OV.htseq_fpkm.tsv 
  563  cd perl
  564  ls
  565  vim locttime.pl
  566  pwel locttime.pl 
  567  perl locttime.pl 
  568  vim locttime.pl
  569  perl locttime.pl 
  570  vim locttime.pl
  571  perl locttime.pl 
  572  cd /mnt/hgfs/Ubunsave/getGTExNormal
  573  ls
  574  cat -A gtex_RSEM_gene_fpkm.tsv 
  575  clear
  576  ls
  577  sed -n l gtex_RSEM_gene_fpkm.tsv 
  578  clear
  579  ls
  580  vim *.pl
  581  perl GTEx.getGTExNormal.pl 
  582  vim *.pl
  583  perl GTEx.getGTExNormal.pl 
  584  vim *.pl
  585  cd /mnt/hgfs/Ubunsave/getGTExNormal
  586  perl localtime(time)
  587  perl localtime()
  588  perl localtime
  589  ls
  590  perl time.pl 
  591  ls
  592  perl GTEx.getGTExNormal.pl 
  593  cd /mnt/hgfs/Ubunsave/tcga
  594  perl GTEx.group.pl TCGA-OV.htseq_fpkm.tsv 
  595  cd python/
  596  ls
  597  python firsttest.py 
  598  python foru.py 
  599  python p.py 
  600  python rose.py 
  601  python threetest.py 
  602  python twotest.py 
  603  vim rose.py 
  604  ls
  605  vim threetest.py 
  606  history
  607  conda env list
  608  conda activate bio
  609  conda list
  610  conda env list
  611  conda activate py36
  612  conda list
  613  bwa -v
  614  bwa -h
  615  bwa -V
  616  bowtie2  -v
  617  bowtie2  -h
  618  ls
  619  history
  620  ls
  621  history
  622  cd python/
  623  ls
  624  python p.py 
  625  python twotest.py 
  626  python firsttest.py 
  627  cd .//
  628  cd ../
  629  ls
  630  wget https://www.encodeproject.org/files/ENCFF528RJO/@@download/ENCFF528RJO.fastq.gz
  631  ls
  632  ls -lh
  633  ls -f
  634  ls -a
  635  cd data/human/methy/
  636  ls
  637  wget -c https://www.encodeproject.org/files/ENCFF607XAZ/@@download/ENCFF607XAZ.bam
  638  conda env list
  639  conda activate py36
  640  cd python/
  641  ls
  642  conda env list
  643  conda list
  644  conda activate bio
  645  conda list
  646  conda env list
  647  conda activate py36
  648  conda list
  649  conda activate base
  650  conda list
  651  conda activate bio
  652  conda list
  653  conda activate py36
  654  conda search gatk
  655  cd GATK/
  656  ls
  657  unzip gatk-4.1.9.0.zip 
  658  cd gatk-4.1.9.0/
  659  ls
  660  gatk --help
  661  gatk -v
  662  gatk
  663  ./gatk --help
  664  echo $PATH
  665  pwd
  666  echo export PATH="/home/yuan/GATK/gatk-4.1.9.0:$PATH" >> ~/.bashrc
  667  echo $PATH
  668  source .bashrc
  669  source ~/.bashrc
  670  echo $PATH
  671  gatk --help
  672  gatk -v
  673  conda activate base
  674  gatk
  675  gatk --list
  676  gatk
  677  vim ~/.bashrc
  678  gatk
  679  echo $PATH
  680  vim ~/.bashrc
  681  source ~/.bashrc
  682  gatk
  683  echo export PATH="/home/yuan/biosoft/GATK/gatk-4.1.9.0:$PATH" >> ~/.bashrc
  684  source ~/.bashrc
  685  gatk
  686  gatk Tool --help
  687  cd 
  688  cd /home/yuan/data/human/dna/bwa/ENCFF283GNM.bam
  689  cd /home/yuan/data/human/dna/bwa
  690  ls
  691  head ENCFF283GNM.bam 
  692  ls
  693  head ENCFF283GNM.sam 
  694  head -100 ENCFF283GNM.sam 
  695  bwa -h
  696  bwa --help
  697  conda list
  698  conda activate bio
  699  conda list
  700  samtools sort ENCFF283GNM.bam -o ENCFF283GNM.sort.bam 
  701  ls
  702  ls -lh
  703  samtools index ENCFF283GNM.sort.bam 
  704  ls
  705  samtools flagstat ENCFF283GNM.sort.bam
  706  Gatk MarkDuplicates –I ${.sorted.bam} –O ${.sorted.marked.bam}-M { .txt}
  707  gatk MarkDuplicates –I ENCFF283GNM.sort.bam –O ENCFF283GNM.sorted.marked.bam -M ENCFF283GNM.txt
  708  LS
  709  ls
  710  gatk MarkDuplicates –I ENCFF283GNM.sort.bam –O ENCFF283GNM.sorted.marked.bam
  711  gatk MarkDuplicates –I {ENCFF283GNM.sort.bam} -O {ENCFF283GNM.sort.marked.bam} -M {result.txt}
  712  gatk --help
  713  man gatk
  714  gatk
  715  gatk --java-options "-Xmx4g" HaplotypeCaller     -R Homo_sapiens_assembly38.fasta    -I input.bam    -O output.g.vcf.gz    -ERC GVCF
  716  cd data/human/dna/
  717  ls
  718  cd bwa/
  719  ls
  720  gatk --java-options "-Xmx4g" HaplotypeCaller     -R hg19.fa    -I ENCFF283GNM.bam    -O output.g.vcf.gz    -ERC GVCF
  721  gatk --java-options "-Xmx4g" HaplotypeCaller     -R /home/yuan/index/human/bwa/hg19.fa    -I ENCFF283GNM.bam    -O output.g.vcf.gz    -ERC GVCF
  722  ls
  723  head -100 ENCFF283GNM.sam 
  724  gatk
  725  ls
  726  conda env list
  727  conda activate bio
  728  conda list
  729  conda install -y snpeff vcftools bcftools multiqc qualimap
  730  conda list
  731  gatk --help
  732  df
  733  df -hl
  734  conda env list
  735  conda list
  736  conda activate bio
  737  conda list
  738  conda activate py27
  739  conda list
  740  conda env list
  741  conda activate py36
  742  conda list
  743  gatk
  744  gatk --list
  745  conda activate bio
  746  gatk --list
  747  user
  748  sudo
  749  su root
  750  sudo passwd root
  751  su root
  752  conda search fastqc
  753  conda  search python
  754  conda search python
  755  conda install python
  756  wget https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE147276
  757  wget https://ftp.ncbi.nlm.nih.gov/geo/series/GSE18nnn/GSE18520/matrix/
  758  wget https://ftp.ncbi.nlm.nih.gov/geo/series/GSE18nnn/GSE18520/matrix/GSE18520_series_matrix.txt.gz
  759  apt-get search python
  760  apt-get -h
  761  apt-get source python
  762  ip -a
  763  ipconfig
  764  ifconfig
  765  sudo apt install net-tools
  766  ifconfig
  767  users
  768  conda search python
  769  conda search gatk
  770  conda config --add channels https://mirrors.ustc.edu.cn/anaconda/pkgs/free/
  771  conda config --add channels https://mirrors.ustc.edu.cn/anaconda/pkgs/main/
  772  conda config --set show_channel_urls yes
  773  conda config --add channels https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/
  774  conda config --add channels https://mirrors.ustc.edu.cn/anaconda/cloud/msys2/
  775  conda config --add channels https://mirrors.ustc.edu.cn/anaconda/cloud/bioconda/
  776  conda config --add channels https://mirrors.ustc.edu.cn/anaconda/cloud/menpo/
  777  conda search gatk
  778  ls
  779  cd miniconda3/
  780  ls
  781  conda config --add channels conda-forge
  782  conda config --add channels bioconda
  783  conda config --add channels r
  784  conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
  785  conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
  786  conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
  787  conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda 
  788  conda config --set show_channel_urls yes
  789  conda search python
  790  conda config --show-sources
  791  vim /home/yuan/.condarc 
  792  conda search python
  793  vim /home/yuan/.condarc 
  794  conda search python
  795  conda search gatk
  796  conda search GATK
  797  conda search *gatk*
  798  conda search fastqc
  799  conda search r
  800  conda search bwa
  801  conda search mysql
  802  conda search php
  803  conda search r
  804  conda config --add channels https://mirrors.ustc.edu.cn/anaconda/cloud/bioconda/
  805  conda search fastqc
  806  conda config --set show_channel_urls yes
  807  conda search gatk
  808  conda config --show  channels
  809  conda search python
  810  conda search r
  811  conda env list
  812  gatk
  813  gatk --list
  814  cd data/GATK/
  815  ls
  816  wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/006/825/GCF_000006825.1_ASM682v1/GCF_000006825.1_ASM682v1_genomic.fna.gz
  817  gunzip GCF_000006825.1_ASM682v1_genomic.fna.gz
  818  mv GCF_000006825.1_ASM682v1_genomic.fna PM70.fasta
  819  ls
  820  head *
  821  INDEX=/home/yangzhishuang/data/tem/GATK/PM70
  822  pwd
  823  INDEX=/home/yuan/data/GATK/PM70
  824  INDEX
  825  tree
  826  conda list
  827  conda env list
  828  conda activate bio
  829  conda list
  830  conda env list
  831  conda activate py36
  832  conda list
  833  conda install fastp
  834  apt-get install fastp
  835  sudo install fastp
  836  install fastp
  837  conda search fastp
  838  cd data/GATK/
  839  ls
  840  wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/845/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna.gz
  841  ls
  842  ls -lh
  843  ls
  844  samtools faidx E.coli_K12_MG1655.fa
  845  conda activate py36
  846  samtools faidx E.coli_K12_MG1655.fa
  847  conda activate bio
  848  samtools faidx E.coli_K12_MG1655.fa
  849  ls
  850  wget ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR177/SRR1770413/SRR1770413.sra
  851  fastq-dump --split-files SRR1770413
  852  cd input/E.coli/fasta/
  853  fastq-dump --split-files SRR1770413
  854  ls
  855  fastq-dump --split-files SRR1770413
  856  fastq-dump --split-files SRR1770413.sra 
  857  ls
  858  head SRR1770413_1.fastq 
  859  head -100 SRR1770413_1.fastq 
  860  bgzip -f SRR1770413_1.fastq
  861  sudo apt install tabix
  862  bgzip -f SRR1770413_1.fastq
  863  bgzip -f SRR1770413_2.fastq
  864  bwa index E.coli_K12_MG1655.fa
  865  ls
  866  ls -l
  867  vim bwa_and_markdup.sh
  868  ls -l
  869  vim ~/data/GATK/bin/bwa_and_markdup.sh 
  870  sh ~/data/GATK/bin/bwa_and_markdup.sh 
  871  pwd
  872  cd ~
  873  pwd
  874  vim ~/data/GATK/bin/bwa_and_markdup.sh 
  875  cd /home/yuan/data/GATK/input/E.coli/fasta
  876  sh ~/data/GATK/bin/bwa_and_markdup.sh 
  877  vim ~/data/GATK/bin/bwa_and_markdup.sh 
  878  sh ~/data/GATK/bin/bwa_and_markdup.sh 
  879  vim ~/data/GATK/bin/bwa_and_markdup.sh 
  880  sh ~/data/GATK/bin/bwa_and_markdup.sh 
  881  ls -l
  882  gatk CreateSequenceDictionary -R E.coli_K12_MG1655.fa -O E.coli_K12_MG1655.dict && echo "** dict done **"
  883  ls -l
  884  vim ~/data/GATK/bin/gatk.sh 
  885  sh ~/data/GATK/bin/gatk.sh
  886  vim ~/data/GATK/bin/gatk.sh 
  887  sh ~/data/GATK/bin/gatk.sh
  888  ls
  889  cd ../
  890  ls
  891  cd ../
  892  ls
  893  cd output/
  894  ls
  895  cd *
  896  ls
  897  ls -l
  898  head E_coli_K12.g.vcf
  899  head -100 E_coli_K12.g.vcf
  900  head -1000 E_coli_K12.g.vcf
  901  bwa
  902  history
  903  cd index/E.coli/
  904  LS
  905  ls
  906  bwa index E.coli_K12_MG1655.fa
  907  ls
  908  ls -l
  909  cd index/
  910  ls
  911  cd cd E.coli/
  912  ls
  913  cd E.coli/
  914  ls
  915  mkdir bowtie
  916  ls
  917  boetie
  918  conda activate py27
  919  boetie
  920  condaenv list
  921  conda env list
  922  conda acticate py36
  923  conda activate py36
  924  boetie
  925  conda activate bio
  926  boetie
  927  conda activate py27
  928  conda list
  929  conda activate bio
  930  conda list
  931  conda activate  py36
  932  conda list
  933  bowtie2
  934  ls
  935  bowtie2-build E.coli_K12_MG1655.fa ./E.coli_K12_MG1655
  936  bowtie2-build E.coli_K12_MG1655.fa ./bowtie/E.coli_K12_MG1655
  937  cd
  938  cd data/
  939  ls
  940  cd 20201217_wgs_E.coli/
  941  ls
  942  cd input/
  943  ls
  944  gatk
  945  samtools faidx ~/index/E.coli/E.coli_K12_MG1655.fa
  946  conda activate base
  947  samtools faidx ~/index/E.coli/E.coli_K12_MG1655.fa
  948  conda activate bio
  949  samtools faidx ~/index/E.coli/E.coli_K12_MG1655.fa
  950  fastq-dump --split-files SRR1770413.sra
  951  vim ../code/bwa_and_markdup.sh 
  952  sh ../code/bwa_and_markdup.sh 
  953  /home/yuan/biosoft/GATK/gatk-4.1.9.0/gatk CreateSequenceDictionary -R /home/yuan/index/E.coli/E.coli_K12_MG1655.fa -O /home/yuan/index/E.coli/E.coli_K12_MG1655.dict && echo "** dict done **"
  954  vim ../code/gatk.sh 
  955  sh ../code/gatk.sh 
  956  vim ../code/gatk.sh 
  957  sh ../code/gatk.sh 
  958  vim ../code/gzVCF.sh
  959  sh ../code/gzVCF.sh
  960  tree /home/yuan/data/20201217_wgs_E.coli/
  961  sudo apt install tree
  962  tree /home/yuan/data/20201217_wgs_E.coli/
  963  /home/yuan/biosoft/GATK/gatk-4.1.9.0/gatk
  964  gatk Tool
  965  vim ../code/variant_filtration.sh
  966  sh ../code/variant_filtration.sh
  967  vim ../code/variant_filtration.sh
  968  sh ../code/variant_filtration.sh
  969  vim ../code/variant_filtration.sh
  970  /home/yuan/biosoft/GATK/gatk-4.1.9.0/gatk SelectVariants     -select-type INDEL     -V /home/yuan/data/20201217_wgs_E.coli/output/E_coli_K12.vcf.gz     -O /home/yuan/data/20201217_wgs_E.coli/output/E_coli_K12.indel.vcf.gz
  971  /home/yuan/biosoft/GATK/gatk-4.1.9.0/gatk VariantFiltration     -V /home/yuan/data/20201217_wgs_E.coli/output/E_coli_K12.indel.vcf.gz     --filter-expression "QD < 2.0 || FS > 200.0 || SOR > 10.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0"     --filter-name "PASS"     -O /home/yuan/data/20201217_wgs_E.coli/output/E_coli_K12.indel.filter.vcf.gz
  972  /home/yuan/biosoft/GATK/gatk-4.1.9.0/gatk MergeVcfs     -I /home/yuan/data/20201217_wgs_E.coli/output/E_coli_K12.snp.filter.vcf.gz     -I /home/yuan/data/20201217_wgs_E.coli/output/E_coli_K12.indel.filter.vcf.gz     -O /home/yuan/data/20201217_wgs_E.coli/output/E_coli_K12.filter.vcf.gz
  973  time /home/yuan/biosoft/GATK/gatk-4.1.9.0/gatk MergeVcfs     -I /home/yuan/data/20201217_wgs_E.coli/output/E_coli_K12.snp.filter.vcf.gz     -I /home/yuan/data/20201217_wgs_E.coli/output/E_coli_K12.indel.filter.vcf.gz     -O /home/yuan/data/20201217_wgs_E.coli/output/E_coli_K12.filter.vcf.gz
  974  sh ../code/variant_filtration.sh
  975  vim ../code/variant_filtration.sh
  976  /home/yuan/biosoft/GATK/gatk-4.1.9.0/gatk MergeVcfs     -I /home/yuan/data/20201217_wgs_E.coli/output/E_coli_K12.snp.filter.vcf.gz     -I /home/yuan/data/20201217_wgs_E.coli/output/E_coli_K12.indel.filter.vcf.gz     -O /home/yuan/data/20201217_wgs_E.coli/output/E_coli_K12.filter.vcf.gz
  977  /home/yuan/biosoft/GATK/gatk-4.1.9.0/gatk SelectVariants     -select-type INDEL     -V /home/yuan/data/20201217_wgs_E.coli/output/E_coli_K12.vcf.gz     -O /home/yuan/data/20201217_wgs_E.coli/output/E_coli_K12.indel.vcf.gz
  978  /home/yuan/biosoft/GATK/gatk-4.1.9.0/gatk VariantFiltration     -V /home/yuan/data/20201217_wgs_E.coli/output/E_coli_K12.indel.vcf.gz     --filter-expression "QD < 2.0 || FS > 200.0 || SOR > 10.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0"     --filter-name "PASS"     -O /home/yuan/data/20201217_wgs_E.coli/output/E_coli_K12.indel.filter.vcf.gz
  979  /home/yuan/biosoft/GATK/gatk-4.1.9.0/gatk MergeVcfs     -I /home/yuan/data/20201217_wgs_E.coli/output/E_coli_K12.snp.filter.vcf.gz     -I /home/yuan/data/20201217_wgs_E.coli/output/E_coli_K12.indel.filter.vcf.gz     -O /home/yuan/data/20201217_wgs_E.coli/output/E_coli_K12.filter.vcf.gz
  980  # 使用SelectVariants，选出SNP
  981  time /home/yuan/biosoft/GATK/gatk-4.1.9.0/gatk SelectVariants     -select-type SNP     -V /home/yuan/data/20201217_wgs_E.coli/output/E_coli_K12.vcf.gz     -O /home/yuan/data/20201217_wgs_E.coli/output/E_coli_K12.snp.vcf.gz
  982  # 为SNP作硬过滤
  983  time /home/yuan/biosoft/GATK/gatk-4.1.9.0/gatk VariantFiltration     -V /home/yuan/data/20201217_wgs_E.coli/output/E_coli_K12.snp.vcf.gz     --filter-expression "QD < 2.0 || MQ < 40.0 || FS > 60.0 || SOR > 3.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0"     --filter-name "PASS"     -O /home/yuan/data/20201217_wgs_E.coli/output/E_coli_K12.snp.filter.vcf.gz
  984  # 使用SelectVariants，选出Indel
  985  time /home/yuan/biosoft/GATK/gatk-4.1.9.0/gatk SelectVariants     -select-type INDEL     -V /home/yuan/data/20201217_wgs_E.coli/output/E_coli_K12.vcf.gz     -O /home/yuan/data/20201217_wgs_E.coli/output/E_coli_K12.indel.vcf.gz
  986  # 为Indel作过滤
  987  time /home/yuan/biosoft/GATK/gatk-4.1.9.0/gatk VariantFiltration     -V /home/yuan/data/20201217_wgs_E.coli/output/E_coli_K12.indel.vcf.gz     --filter-expression "QD < 2.0 || FS > 200.0 || SOR > 10.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0"     --filter-name "PASS"     -O /home/yuan/data/20201217_wgs_E.coli/output/E_coli_K12.indel.filter.vcf.gz
  988  # 重新合并过滤后的SNP和Indel
  989  time /home/yuan/biosoft/GATK/gatk-4.1.9.0/gatk MergeVcfs     -I /home/yuan/data/20201217_wgs_E.coli/output/E_coli_K12.snp.filter.vcf.gz     -I /home/yuan/data/20201217_wgs_E.coli/output/E_coli_K12.indel.filter.vcf.gz     -O /home/yuan/data/20201217_wgs_E.coli/output/E_coli_K12.filter.vcf.gz
  990  gatk -list
  991  ls
  992  pwd
  993  cd ~/data/20201217_wgs_clean/
  994  cd input/
  995  wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/006/825/GCF_000006825.1_ASM682v1/GCF_000006825.1_ASM682v1_genomic.fna.gz
  996  gunzip GCF_000006825.1_ASM682v1_genomic.fna.gz
  997  mv GCF_000006825.1_ASM682v1_genomic.fna PM70.fasta
  998  vim ../code/gatk1.sh
  999  cd ../base/
 1000  samtools
 1001  bowtie2
 1002  conda list
 1003  conda env list
 1004  conda activate bio
 1005  conda list
 1006  conda env list
 1007  conda activate py27
 1008  conda list
 1009  conda env list
 1010  conda activate py36
 1011  conda list
 1012  conda activate py27
 1013  conda list
 1014  history
 1015  history > history.sh
